Matter 2 provides an updated and more robust C++ backend to matter objects, along with a completely new implementation of sparse arrays and new signal processing functions for nonuniform sparse signal data.
Originally designed as a backend for the Cardinal package, The first version of Matter was constantly evolving to handle the ever-increasing demands of larger-than-memory mass spectrometry (MS) imaging experiments. While it was designed to be flexible from a user’s point-of-view to handle a wide array for file structures beyond the niche of MS imaging, its codebase was becoming increasingly difficult to maintain and update.
Matter 2 was re-written from the ground up to simplify some features that were rarely needed in practice and to provide a more robust and future-proof codebase for further improvement.
Matter can be installed via the BiocManager package.
install.packages("BiocManager")
BiocManager::install("matter")The same function can be used to update Matter and other Bioconductor packages.
Once installed, Matter can be loaded with library():
library(matter)Coming soon…..
Coming soon…..
Coming soon…..
sessionInfo()## R Under development (unstable) (2022-10-25 r83175)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.1 LTS
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## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.17-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
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## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
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## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
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## other attached packages:
## [1] matter_2.1.0 Matrix_1.5-1 BiocParallel_1.33.0
## [4] BiocStyle_2.27.0
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## loaded via a namespace (and not attached):
## [1] cli_3.4.1 knitr_1.40 rlang_1.0.6
## [4] xfun_0.34 ProtGenerics_1.31.0 DBI_1.1.3
## [7] stringi_1.7.8 jsonlite_1.8.3 htmltools_0.5.3
## [10] sass_0.4.2 rmarkdown_2.17 grid_4.3.0
## [13] evaluate_0.17 jquerylib_0.1.4 fastmap_1.1.0
## [16] yaml_2.3.6 bookdown_0.29 BiocManager_1.30.19
## [19] stringr_1.4.1 compiler_4.3.0 codetools_0.2-18
## [22] irlba_2.3.5.1 lattice_0.20-45 digest_0.6.30
## [25] R6_2.5.1 parallel_4.3.0 magrittr_2.0.3
## [28] bslib_0.4.0 tools_4.3.0 biglm_0.9-2.1
## [31] BiocGenerics_0.45.0 cachem_1.0.6